I'm sure Mr. Mullen will check in here however as I understand it, the SA does not DQ candidates, DoDMERB does. Although your DS applied to USAFA, it is DoDMERB that does the initial medical evaluation. Be assured, if the candidate is competitive for an appointment, the SA will request a waiver review. The waiver review process is very thorough - if they request it you will have ample opportunity to respond with additional information.
You could search for a thread "DQ Advice for Parents" that covers the process as our DS went through it for USAFA and has some similarities to your situation (though remember, there are hundreds of variables and each situation is completely unique.) Also reviewing the other threads in the DoDMERB forum will probably be helpful. Then at least you'll have a broad understanding of the process and you can focus on specifics with Mr. Mullen. Assuming you're referring to Class of 2026? If so, deep breaths and pace yourself, it's a long journey.